Setup

Setting up a simulation model

It will normally be necessary to follow steps 1 to 6 of the PDB Files tutorial
when setting up a simulation model for a protein from a PDB file.
However, in this case, the proteins are very simple — consisting of only
standard
amino acid residues — and perusal of the structures indicates
that there are no non-hydrogen atoms with undefined coordinates. This
means that the much simpler approach of Example 19 in the pDynamo
distribution suffices to generate
molecular mechanics models of the proteins.

Example program:Setup.py

Each of the PDB files contains several structural models, as is
often the case with protein structures determined via NMR spectroscopy.
By default, the PDBFile_ToSystem method will take the structure of the first model from the file. To
explicitly specify that the nth model be chosen, employ the argument modelNumber = n (noting that n starts at one).